Documentation for Strengths

Here is the documentation for the Strengths package.

• The Strengths Package
  • Introduction
  • Installing and using Strengths
  • Documentation
  • Source code and contribution
  • Testing
  • License
  • Initial authors
  • All authors
• Using Strengths
  • Installing and importing Strengths
  • The fundamental concepts
    • Object concepts
      • Species (Species class)
      • Reaction (Reaction class)
      • Network (RDNetwork class)
      • Space (RDSpace class)
      • System (RDSystem class)
      • Script (RDScript class)
      • Engine (RDEngineBase derived class)
      • Trajectory (RDTrajectory class)
    • Other concepts
      • Cells
      • Environments
      • Chemostats
  • Building and simulating a reaction-diffusion system
    • A simple example without diffusion
    • Alternative ways to define a reaction-diffusion system
      • Through a JSON File
      • With multiple JSON files
      • With a Python dictionary
      • Using object construction
    • Alternative ways to script a simulation
      • Creating the script
      • Simulating the script
    • Another example featuring diffusion
    • A Third Example with chemostats
    • A fourth example with environments
    • Defining boundary conditions
    • References
  • Setting up initial conditions
    • Setting up the initial state
    • Setting up the chemostates
    • Changing the Species.density attribute
    • Changing the Species.chstt attribute
  • Working the simulation output
    • What is in the simulation output?
    • Accessing trajectory data
    • Examples
      • use case 1: Plotting a trajectory
      • use case 2: Plotting a sampled system state
  • Working with units
    • UnitsValue, UnitArray and Units
    • Operations on UnitValue and UnitArrays
      • addition and subtraction
      • division and multiplication
      • modulo
      • power
      • comparison
  • Using Strengths with SciPy’s integration ODE methods
  • References
  • Simulation Engines
    • What is a simulation engine
    • Engine implementations installed with Strengths
    • References
  • Diffusion in graph spaces
  • References
  • Array indexing
    • Space cell index
    • System state and system chemostats
    • State trajectory data
  • Building Strengths from source
  • Dependencies
    • NumPy
    • Matplotlib
• Dictionary/JSON documentation
  • Reaction-diffusion simulation script
    • “system”:
    • “t_sample”:
    • “time_step”:
    • “sampling_policy”:
    • “sampling_interval”:
    • “t_max”:
    • “rng_seed”:
    • “units”:
  • Reaction-diffusion system
    • “network”:
    • “space”:
    • “state”:
    • “chstt_map”:
    • “units”:
  • Reaction-diffusion network
    • “species”:
    • “reactions”:
    • “environments”:
    • “units”:
  • species
    • “label”:
    • “density”:
    • “D”:
    • “chstt”:
    • “units”:
  • reaction
    • “label”:
    • “stoechiometry”:
    • “k+”:
    • “k-“:
    • “environments”:
    • “units”:
  • Grid space
    • “w”:
    • “h”:
    • “d”:
    • “cell_env”:
    • “cell_volume”:
    • “units”:
  • Units system
    • “space”:
    • “time”:
    • “quantity”:
  • unit array
    • “value”:
    • “units”:
• API Reference
  • Useful info
    • Arrays and numbers
  • Core features
    • Directly imported
      • Reaction-diffusion networks
        • Species
        • Reaction
        • RDNetwork
        • load_rdnetwork()
        • save_rdnetwork()
        • rdnetwork_to_dict()
        • rdnetwork_from_dict()
      • Reaction-diffusion spaces
        • RDGridSpace
        • RDGraphSpace
        • load_rdspace()
        • save_rdspace()
        • rdspace_to_dict()
        • rdspace_from_dict()
      • Reaction-diffusion systems
        • RDSystem
        • generate_species_state()
        • generate_system_state()
        • generate_species_chemostats()
        • generate_system_chemostats()
        • load_rdsystem()
        • save_rdsystem()
        • rdsystem_to_dict()
        • rdsystem_from_dict()
      • Reaction-diffusion simulation script
        • RDScript
        • rdscript_from_dict()
        • rdscript_to_dict()
        • load_rdscript()
        • save_rdscript()
      • Reaction-diffusion system trajectory
        • RDTrajectory
        • save_rdtrajectory()
        • load_rdtrajectory()
        • References
      • Reaction-diffusion simulations
        • simulate()
        • simulate_script()
      • Units
        • UnitsSystem
        • UnitsDimensions
        • Units
        • UnitValue
        • UnitArray
        • density_units_dimensions()
        • volume_units_dimensions()
        • quantity_units_dimensions()
        • space_units_dimensions()
        • time_units_dimensions()
        • parse_units()
        • parse_unitvalue()
        • convert_value()
        • unitssystem_from_dict()
        • unitsdimensions_from_dict()
        • convert_unitvalue()
        • unitarray_from_dict()
        • unitarray_to_dict()
        • References
      • Engine Collection
        • euler_engine()
        • gillespie_engine()
        • tauleap_engine()
      • References
    • Not directly imported
      • Simulation engines
        • RDEngineBase
      • Constants
        • avogadro_number()
      • Kinetics
        • compute_reaction_rates()
        • compute_diffusion_rates()
        • compute_dspeciesdt()
        • compute_dstatedt()
  • Side features
    • Plot
      • plot_trajectory()
      • plot_sample_state_2D()
      • plot_state_2D()
      • plot_environments_2D()
      • plot_chemostats_2D()